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Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 12% PEG 20000, 100mM MES pH6.5, 20% Glycerol, 1.5mM inhibitor 1c
Crystal Properties Matthews coefficient Solvent content 2.52 51.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.88 α = 90 b = 120.22 β = 90 c = 231.89 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 2M 2012-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.100 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.13 44.05 99.3 0.14 0.154 0.063 0.994 9 5.8 93976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.17 90.8 0.876 0.972 0.413 0.61 2 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5YP1 2.13 40 89236 4652 99.23 0.18028 0.17787 0.1853 0.22627 0.2294 RANDOM 32.091
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.76 -0.81 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.277 r_dihedral_angle_4_deg 19.46 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 7.321 r_long_range_B_refined 6.256 r_long_range_B_other 6.232 r_scangle_other 4.744 r_mcangle_it 3.592 r_mcangle_other 3.592 r_scbond_it 3.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.277 r_dihedral_angle_4_deg 19.46 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 7.321 r_long_range_B_refined 6.256 r_long_range_B_other 6.232 r_scangle_other 4.744 r_mcangle_it 3.592 r_mcangle_other 3.592 r_scbond_it 3.148 r_scbond_other 3.148 r_mcbond_it 2.517 r_mcbond_other 2.516 r_angle_refined_deg 1.864 r_angle_other_deg 1.052 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11320 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling MOLREP phasing